"A wanted Palestinian terrorist was killed this morning in Bilin during a gunfight with the army while he was in a cave," tweeted army spokesman Avichay Adraee in Arabic.
The gunfight broke out after troops stormed an area between the villages of Bilin and Kufr Ne'meh, 10 kilometres northwest of Ramallah, shortly before dawn.
The army named the dead man as Mohammed Assi and said he was an Islamic Jihad militant responsible for a bus bombing in Tel Aviv that left 29 people injured.
He said troops had arrested another two people who were also involved in the bombing.
Also Read
Islamic Jihad confirmed Assi was one of their militants in a statement on its website which said he was "assassinated by the occupation in Kufr Ne'meh."
Local witnesses told AFP the incident began at 5:00 am (0200 GMT) when Israeli troops entered Bilin then moved into an area between the village and nearby Kufr Ne'meh, sparking gunfire.
Local witnesses confirmed troops were hunting for Assi, saying he was a wanted Islamic Jihad activist.
The Tel Aviv bombing took place on November 21 on a bus near the defence ministry.
The attack took place as Israel was engaged in a major air campaign in Gaza to stamp out cross-border rocket fire that ended with a mutual ceasefire several hours later.